[gmx-users] pdb2gmx error

[Tsjerk Wassenaar]

No, but you should try to distinguish an O (letter-O) from a 0 (numeric zero).

Tsjerk

On Wed, Mar 19, 2008 at 3:54 PM, Gadzikano Munyuki
<Gadzikano.Munyuki at uct.ac.za> wrote:
> I want to do dynamics on a cyclic polypeptide. The peptide contains a residue that is not standard Ornithine. I have added [ORN] to the ffoplsaa.rtp file and the aminoacids.dat file.I have put these in the working directory and also in the library. If I grep these files [ORN] is there but i still get an error message below.Is there some database i am meant to edit.
>
>
>  Opening library file /usr/share/gromacs/top/FF.dat
>
>  Select the Force Field:
>   0: GROMOS96 43a1 force field
>   1: GROMOS96 43b1 vacuum force field
>   2: GROMOS96 43a2 force field (improved alkane dihedrals)
>   3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
>   4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
>   5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
>   6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>   7: [DEPRECATED] Gromacs force field (see manual)
>   8: [DEPRECATED] Gromacs force field with hydrogens for NMR
>   9: Encad all-atom force field, using scaled-down vacuum charges
>  10: Encad all-atom force field, using full solvent charges
>  6
>  Opening library file ffoplsaa.rtp
>  Opening library file aminoacids.dat
>  Reading FIN.pdb...
>  Read 97 atoms
>  Opening library file /usr/share/gromacs/top/xlateat.dat
>  26 out of 26 lines of xlateat.dat converted succesfully
>  Analyzing pdb file
>  There are 1 chains and 0 blocks of water and 14 residues with 97 atoms
>
>   chain  #res #atoms
>   1 ' '    14     97
>
>  All occupancies are one
>  Opening library file /usr/share/gromacs/top/ffoplsaa.atp
>  Atomtype 817
>  Reading residue database... (ffoplsaa)
>  Opening library file ffoplsaa.rtp
>  Using default: generating 1,4 H--H interactions
>  Using default: removing impropers on same bond as a proper
>  Residue 51
>  Sorting it all out...
>  Opening library file /usr/share/gromacs/top/ffoplsaa.hdb
>  Opening library file /usr/share/gromacs/top/ffoplsaa-n.tdb
>  Opening library file /usr/share/gromacs/top/ffoplsaa-c.tdb
>
>  Back Off! I just backed up topol.top to ./#topol.top.17#
>  Processing chain 1 (97 atoms, 14 residues)
>  There are 16 donors and 13 acceptors
>  There are 15 hydrogen bonds
>  -------------------------------------------------------
>  Program pdb2gmx, VERSION 3.3
>  Source code file: resall.c, line: 438
>
>  Fatal error:
>  Residue '0RN' not found in residue topology database
>
>  -------------------------------------------------------
>
>
>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623